Lake publicly revealed his advanced case of colon cancer.[2] He was diagnosed in April 2008, and it then "progressed from a single tumor to metastatic disease affecting the lung and liver, recurring after multiple surgeries and chemotherapy courses."[3][4][5][6] He used crowd funding through YouCaring to pay for whole genome sequencing, towards the "small possibility that the results of such a test...may suggest a treatment path."[3][4][5][6] Lake died of the illness on June 1, 2014, just five days before his 50th birthday.[7]

Lake is the subject of a documentary called Lakeside – A Year With Jay Lake by Waterloo Productions. The film, which follows Lake's fight against cancer, had a special work-in-progress screening August 30, 2013, at the World Science Fiction Convention in San Antonio.[8][9] As of May 2014[update], it is in post-production and is scheduled to premier at Sasquan in Spokane Washington during the 73rd World Science Fiction Convention on August 21, 2015.[10]

His posthumously published collection Last Plane to Heaven was honored with the 2015 Endeavour Award.[11]

^"Lakeside advanced screening exclusive to LoneStarCon3". Waterloo Productions. Archived from the original on January 19, 2014. Retrieved January 19, 2014. It is with great pleasure that Waterloo Productions, LLC. announces the world premiere on our documentary: LAKESIDE – A Year With Jay Lake. Please join subject Jay Lake and director Donnie G. Reynolds as they introduce the film on Friday August 30th in San Antonio, Texas during WorldCon.